There's transit and there's transit. If I'm connecting to an Amtrak train, would I rather ride a reserved-seat, tour-bus-style coach with underfloor (perhaps checked) baggage space and only one stop between Reading and Philly as part of the trip, or perch in a subway-like car making multiple stops, with no room for luggage? I'm guessing the former, especially since the bus is likely to take a more direct route and arrives/departs the train station in a spot fairly close to the main building?

It's the same issue as with taking transit to/from an airport. If you're not just a day tripper, you have luggage, and most public transit serving airports (and train stations) doesn't have any place for you to put it other than between your knees or on the seat next to you. Uncomfortable, at best.